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Yorodumi- PDB-3eun: Crystal structure of the 2[4Fe-4S] C57A ferredoxin variant from a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eun | ||||||
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Title | Crystal structure of the 2[4Fe-4S] C57A ferredoxin variant from allochromatium vinosum | ||||||
Components | Ferredoxin | ||||||
Keywords | ELECTRON TRANSPORT / FERREDOXIN / [4FE-4S] CLUSTER / 4Fe-4S / Iron / Iron-sulfur / Metal-binding / Transport | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Allochromatium vinosum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å | ||||||
Authors | Saridakis, E. / Mavridis, I.M. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2009 Title: Insight into the protein and solvent contributions to the reduction potentials of [4Fe-4S]2+/+ clusters: crystal structures of the Allochromatium vinosum ferredoxin variants C57A and V13G and ...Title: Insight into the protein and solvent contributions to the reduction potentials of [4Fe-4S]2+/+ clusters: crystal structures of the Allochromatium vinosum ferredoxin variants C57A and V13G and the homologous Escherichia coli ferredoxin. Authors: Saridakis, E. / Giastas, P. / Efthymiou, G. / Thoma, V. / Moulis, J.M. / Kyritsis, P. / Mavridis, I.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eun.cif.gz | 60 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eun.ent.gz | 43.3 KB | Display | PDB format |
PDBx/mmJSON format | 3eun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/3eun ftp://data.pdbj.org/pub/pdb/validation_reports/eu/3eun | HTTPS FTP |
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-Related structure data
Related structure data | 2zvsC 3exyC 1bluS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 9031.938 Da / Num. of mol.: 1 / Mutation: C57A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Allochromatium vinosum (bacteria) / Gene: fdx / Production host: Escherichia coli (E. coli) / References: UniProt: P00208 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.58 % |
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Crystal grow | Temperature: 277 K / pH: 8.5 Details: 3.5M AMMONIUM SULPHATE 0.1 M SODIUM CHLORIDE, 0.1 M TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8081 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 31, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8081 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→50 Å / Num. obs: 54434 / % possible obs: 99.7 % / Redundancy: 6.2 % |
Reflection shell | Resolution: 1.05→1.07 Å / Redundancy: 5.3 % / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BLU Resolution: 1.05→14 Å / Num. parameters: 8225 / Num. restraintsaints: 9285 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF). THE MISSING R-WORK VALUE IS DUE TO THE FACT THAT THE DATA OF THE REFERENCE AND WORKING SETS WERE MERGED IN THE LAST 6 CYCLES OF SHELX ...Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF). THE MISSING R-WORK VALUE IS DUE TO THE FACT THAT THE DATA OF THE REFERENCE AND WORKING SETS WERE MERGED IN THE LAST 6 CYCLES OF SHELX REFINEMENT, SO THERE IS ONLY ONE FINAL R (R = 0.1028 FOR FO>4SIG(FO) AND 0.1159 FOR ALL DATA).
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Refine analyze | Num. disordered residues: 10 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 812.97 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.05→14 Å
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Refine LS restraints |
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